This is the repository for the paper 'Inter-regional correlation estimators for functional magnetic resonance imaging'.

It contains data and code to reproduce the results in the paper.

Organisation

• Output: correlation estimates for the simulation, rat, and human data
• Paper_code: code for the figures in the paper (Rmarkdown)
• R_code: R package implementing correlation estimators.

Installation

The package can be installed with install.packages('./ireco4fmri/R_code/',repos=NULL,type='source')

Data

Rat names

• rat 20160524_153000: dead rat
• rat 20160616_103405: live rat (Eto-L)
• rat 20160615_103000: live rat (Iso-W)

Output files description

Edge_list_Rat_corrfmripaper.txt

File listing the pairs of regions in the order in which the inter-correlations were estimated. Each column corresponds to a pair of regions.

Rat_XXX_Bigregs_CorrEstimates.txt

File storing the correlations computed on rat XXX using the following estimators: "agg", "ave", "aggc", "laveB", "raveB", "lraveB", "saveB", "slaveB", "sraveB", "raveB". There are two columns:

• EST: the name of the estimator,

• CORR: the corresponding correlation coefficient.

Remark: "agg"="CA", "ave"="AC", "raveB"="R", "laveB"="lCA", "lraveB"="lR","saveB"="D", "sraveB"="RD", "slaveB"="lD", "slraveB"="lRD"

Rat_XXX_Bigregs_tscrop1_CorrEstimates.txt

Same type of file as Rat_XXX_Bigregs_CorrEstimates.txt. It corresponds to the correlations estimated on the first half of the time series. The correlations estimated on the second half of the time series are called: Rat_XXX_Bigregs_tscrop2_CorrEstimates.txt.

Directory organization

For the HCP data:

HCP_data
	sub-XXX
		est-AAA
			ses-0
				sub_XXX-est_AAA-ses_0.csv
			ses-1
				sub_XXX-est_AAA-ses_1.csv
		est-BBB
			...
	sub-EEE
		...

where the sub-XXX folders corresponds to subject XXX, est-AAA to correlation estimator AAA, ses-0 and ses-1 to exam0 and exam1 of subject XXX.

Similarly, for the rat data:

Rat_data
	sub-XXX
		est-AAA
			tscrop-1
				sub_XXX-est_AAA-tscrop_1.csv
			tscrop-2
				sub_XXX-est_AAA-tscrop-2.csv
			tsfull
				sub_XXX-est_AAA-tsfull.csv
		est-BBB
			...
	sub-EEE
		...

where the tscrop_1 and tscrop_2 corresponds to the first and second halves of the time series, respectively, and tsfull to the full time series.

The *.csv files contain the correlation matrix of the corresponding subject, session and estimator.